Genetic risk is conferred by subtle differences in the sequence of the genome among individuals in a population. The human genome differs between individuals most frequently due to single nucleotide polymorphisms (SNPs), although other variations are also important. SNPs are located on average every 500 base pairs in the human genome. Accordingly, a typical human gene containing 250,000 base pairs may contain approximately 500 different SNPs. Only a minor number of SNPs are located in exons and alter the amino acid sequence of the protein encoded by the gene. Most SNPs may have no known effect on gene function, while others are known to alter transcription, splicing, translation, or stability of the mRNA encoded by the gene. Additional genetic polymorphisms in the human genome are caused by insertions, deletions, translocations, or inversions of either short or long stretches of DNA.
Parent-of-origin effects (POE) are genetic effects that are transmitted from parents to offspring in such a manner that the expression of the phenotype in the offspring depends on whether the transmission originated from the mother or the father. The effect of a sequence variant in the nuclear genome on the phenotype may depend on its parental origin. In one scenario, the effect is due to imprinting, in which an allele is silenced via an epigentic mechanism such as methylation when inherited from one parent and expressed when inherited from the other parent. In general, however, there are three parent-of-origin effects, i.e. those that arise from epigenetic regulation of gene expression (e.g., imprinting), those that arise from effects of intrauterine environment on the development of the fetus and those that arise from genetic variation in the maternally inherited mitochondrial genome.
Diabetes mellitus, often called diabetes, is a metabolic disease wherein carbohydrate utilization is reduced and lipid and protein utilization is enhanced, and is caused by an absolute or relative deficiency of insulin. In the more severe cases, diabetes is characterized by chronic hyperglycemia, glycosuria, water and electrolyte loss, ketoacidosis and coma. Long term complications can include development of both microvascular complications such as neuropathy, retinopathy and nephropathy and macrovascular complications such as myocardial infarction (MI), stroke and peripheral arterial disease (PAD), caused by generalized degenerative changes in large and small blood vessels. The most common form of diabetes is type 2 diabetes (T2D), (also called non-insulin-dependent diabetes) which is characterized by hyperglycemia due to impaired insulin secretion and insulin resistance in target tissues and increased glucose output by the liver. Both genetic and environmental factors contribute to T2D. For example, obesity plays a major role in the development of T2D. Type 1 diabetes is characterized by loss of insulin-producing beta cells in the islets of Langerhans, leading to insulin deficiency, and represents a majority of diabetes cases affecting children.
The prevalence of T2D worldwide is currently 6% but is projected to rise over the next decade (Amos, A. F., McCarty, D. J., Zimmet, P., Diabet Med 14 Suppl 5, S1 (1997)). This increase in prevalence of T2D is attributed to increasing age of the population and rise in obesity. The health implications of T2D are enormous. In 1995, there were 135 million adults with the disease worldwide. It is estimated that close to 300 million will have T2D in the year 2025 (King, H., et al., Diabetes Care, 21(9): 1414-1431 (1998)). The prevalence of T2D in the adult population in Iceland is 2.5% (Vilbergsson, S., et al., Diabet. Med., 14(6): 491-498 (1997)), which means that approximately 5,000 people over the age of 34 in Iceland have T2D.
Many T2D patients suffer serious complications of chronic hyperglycemia including microvascular complications (nephropathy, neuropathy, retinopathy) and accelerated development of cardiovascular disease (including cerebrovascular disease (stroke), myocardial infarction, and peripheral arterial disease) through macrovascular complications.
In fact, the enormous public health burden of diabetes is largely due to the development of vascular complications of the disease. Cardiovascular disease (CVD) is a major complication and the leading cause of premature death among people with diabetes and accounts for over 75% of all deaths among diabetics. Adults with diabetes are two to four times more likely to have heart disease or suffer a stroke than people without diabetes. Approximately 35% of type 1 diabetes patients die from a cardiovascular disease before age 55, illustrating the devastating consequence of the disease through its cardiovascular complications (Krolewski, A. S. et al. N Engl J Med 317:1390-8 (1987)). The overall prevalence of cardiovascular disease is over 55% in adults with diabetes as compared with 2%-4% of the general population (Asley, R. Levy, A. P. Vasc Health Risk Man 1:19-28 (2005)).
Diabetic retionpathy is the cause of blindness in about 5% of blind people worldwide, and almost everyone with diabetes has some degree of retinopathy after 20 years with the disease (Marshall, S. M. Flyvbjerg, A. British Med J 333:475-80 (2006)). The prevalence of retinopathy is highest in young-onset patients, and steadily increase with duration of diabetes (Chiarelli, F., et al. Horm Res 57(suppl 1):113-6 (2002)).
Nephropathy is also common in diabetic patients, which confers increased risk of premature death due to end-stage renal failure and cardiovascular disease. About half of diabetic patients develop microalbuminuria, which is a marker for early nephropathy, at some point, and about one third will progress to proteinuria. Once present, proteinuria will inevitably lead to end stage renal disease; between 20% and 50% of patients who start renal replacement therapy have diabetes (Marshall, S. M. Flyvbjerg, A. British Med J 333:475-80 (2006)). Patients with diabetes have between 30% and 50% lifetime risk of developing chronic peripheral neuropathy, which can lead to severe symptoms such as foot ulcerations and amputation of lower limbs.
Many of the complications of diabetes have a prolonged subclinical asymptomatic phase. Thus, screening for presymptomatic complications, such as retinopathy and microalbuminuria is extremely important for effective disease management. For example, the micro- and macrovascular complications of diabetes are almost unknown in younger children and rare in adolescents and young adults, but can be detected as soon as 2-5 years after diagnosis during childhood and adolescence (Clarke B. F., in Diabetes Mellitus in Children and Adolescents, Kelnar, C. (ed); London, Chapman & Hall, pp 539-51 (1994)).
As genetic polymorphisms conferring risk of common diseases, such as Type 1 and Type 2 diabetes mellitus, are uncovered, genetic testing for such risk factors is becoming important for clinical medicine. Established examples include apolipoprotein E testing to identify genetic carriers of the apoE4 polymorphism in dementia patients for the differential diagnosis of Alzheimer's T2D, and of Factor V Leiden testing for predisposition to deep venous thrombosis. More importantly, in the treatment of cancer, diagnosis of genetic variants in tumor cells is used for the selection of the most appropriate treatment regime for the individual patient. In breast cancer, genetic variation in estrogen receptor expression or heregulin type 2 (Her2) receptor tyrosine kinase expression determine if anti-estrogenic drugs (tamoxifen) or anti-Her2 antibody (Herceptin) will be incorporated into the treatment plan. In chronic myeloid leukemia (CML) diagnosis of the Philadelphia chromosome genetic translocation fusing the genes encoding the Bcr and Abl receptor tyrosine kinases indicates that Gleevec (STI571), a specific inhibitor of the Bcr-Abl kinase should be used for treatment of the cancer. For CML patients with such a genetic alteration, inhibition of the Bcr-Abl kinase leads to rapid elimination of the tumor cells and remission from leukemia.
Until recently, two approaches were mainly used to search for genes associated with T2D. Single nucleotide polymorphisms (SNPs) within candidate genes have been tested for association and two variants conferring a modest risk of T2D were identified by this method; a protective Pro12Ala polymorphism in the peroxisome proliferator activated receptor gamma gene (PPARG2) (Altshuler, D. et al., Nat Genet. 26, 76 (2000)) and a polymorphism in the potassium inwardly-rectifying channel, subfamily J, member 11 gene (KCNJ11) (Gloyn A. L. et al., Diabetes 52, 568 (2003)). Genome-wide linkage scans in families with the common form of T2D have yielded several loci but the responsible genes within these loci have mostly yet to be uncovered. The rare Mendelian forms of T2D, namely maturity-onset diabetes of the young (MODY), have yielded six genes by positional cloning (Gloyn, A. L., Ageing Res Rev 2, 111 (2003)).
Genome-wide linkage scan for T2D in the Icelandic population showed suggestive evidence of linkage to chromosome 10q (Reynisdottir, I. et al., Am J Hum Genet. 73, 323 (2003)). Fine mapping of this locus revealed the transcription factor 7-like 2 gene (TCF7L2; formerly TCF4) as being associated with T2D (P=2.1×10(−9)) (Grant, S. F. et al., Nat Genet. 38, 320 (2006)). Compared with non-carriers, heterozygous and homozygous carriers of the at-risk alleles (38% and 7% of the population, respectively) have relative risks of 1.45 and 2.41. This corresponds to a population attributable risk of 21%. Association of the TCF7L2 variant has now been replicated in a large number of independent studies with similar relative risk found in the different populations studied. The TCF7L2 gene product is a high mobility group box-containing transcription factor previously implicated in blood glucose homeostasis. It is thought to act through regulation of proglucagon gene expression in enteroendocrine cells via the Wnt signaling pathway.
Recently, genome wide association studies using a large number (300,000-1,000,000) of SNPs have been applied to T2D (Sladek, R et al. Nature. 2007; 445:828-30; Steinthorsdottir V et al. Nat. Gen. 2007; 39:770-5; Saxena, R et al. Science 2007; 316:1331-6; Zeggini, E et al. Science 2007; 316:1336-41; Scott, L J et al. Science 2007; 316:1341-5; Zeggini, E et al. Nat. Gen. 40:638-45 (2008). In addition to confirming the three previously identified variants (PPARG, KCNJ11 and TCF7L2) these studies have thus far identified 11 additional genetic variants conferring risk of T2D. All the variants have a modest risk with TCF7L2 conferring the highest risk. Most, if not all, genome wide studies published to date treat the paternal and maternal alleles as interchangeable. This is likely due to the fact that unless the parents of a proband have been genotyped, the information required to determine the parental origin of alleles is unavailable.
Despite the advances in unraveling the genetics of T2D, the pathophysiology of the T2D remains elusive. However, with the current genetic information we are in a better position to test the effect of different treatment options in relation to the genetic background. It has already been shown that the TCF7L2 at-risk genotype affects the treatment outcome both from lifestyle changes and medication (Florez J C et al. N Engl J Med 2006; 355:241-50; Pearson E R et al. Diabetes 2007; 2178-82).
While our understanding of the genetic bases of developing T2D has increased, the genetics of the disease are still not fully explained. There is therefore an unmet medical need to define additional genetic risk factors affecting the development of T2D. Such information could then be used for diagnostic applications, including applications for identifying those at particularly high risk of developing T2D, development of risk management methods, and for risk stratification where individuals at high risk would be targeted for stringent treatment of other risk factors such as glycemia, high cholesterol and hypertension.